The students, carrying placards -- that read "Don't create crisis", "Honour dignity of Nepalese", "Ensure child right", and "Stop India s blockade" among others -- encircled Kathmandu's Ring Road to demand the immediate lifting of the over two-month-old blockade.
They urged the Madhesi parties to withdraw their agitation and safeguard child rights.
"Stop the blockade. Education is our right," chanted the students. "Let's live and let's study," was their main slogan.
School administrations say the fuel crisis has made it extremely difficult to operate school buses and the shortage of cooking gas was creating problems for students living in hostels.
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Schools were closed for more than two weeks before Diwali as a result of fuel shortage.
According to chairman of the National Private and Boarding Schools Association Karna Bahadur Shahi, 500,000 students from a number of schools from Kathmandu took part in the protests.
Madhesi groups have been staging protests against the seven-province model of the Constitution.
The major demands of the Madhesi people are to re-draw the federal provinces by separating the Terai plains from the hilly region and provide more rights and representation to them.
At least 50 people have been killed in the protests since August.